Well the Maquis ships were stated to be "modified old support couriers" I'd find it more likely the Federation saw how effective they were as fighter craft and began to mass produce them with the Dominion war clouds on the horizon.

But as for the Maquis against the Federation? They started out attacking only Cardassian targets. The Federation just repeatedly interfered, attacked them at every oppurtunity, and the such. You do get the impression they weren't actively targetting the Federation until Eddington took over though, which did up the ante to say the least, but can't be surprising in hindsight.